Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing
This repository contains the supplementary data and methods for Felker 2023 et al. Of primary interest is the supplementary data in TSV (Supp. Table 1) and BED (Supp Table 2, 3) format. The tables describe hg38 genomic coordinates of intronic regions that may be affected by clinically-relevant poison exon inclusion Regions were identified via conservation to mouse cortex RNAseq data (Yan et al. 2015) and annotated with data from OMIM and SFARI genes to determine potential clinical relevance.
Supplementary data for Felker et al.
- Supplementary Table 1 (PE-associated intronic regions of interest and annotations)
- Poison Exons cassettes BED file (hg38)
- PE-associated intronic regions BED file (hg38)
For column descriptions, see data/README.md
Supplementary Tables 2 and 3 are available as UCSC Genome Browser Custom Tracks at these URLs: https://raw.githubusercontent.com/HudsonAlpha/poison_exon_variant_analysis/main/data/tracks/Felker2023SuppelementaryTable2_hg38_PE_cassettes.bed https://raw.githubusercontent.com/HudsonAlpha/poison_exon_variant_analysis/main/data/tracks/Felker2023SuppelementaryTable3_hg38_PE_containing_elements.bed
Supplementary methods for Felker et al. 2023, Poison exon annotations improve the yield of clinically relevant variants in genomic diagnostic testing. Contains local code (R, Bash) and AnVIL code (Docker, WDL) used to generate PE regions of interest, extract VCF variants based on these regions, annotate, and filter to variants of interest for manual review.
For more detail, see scripts/README.md
https://www.biorxiv.org/content/10.1101/2023.01.12.523654v1
First author: Stephanie Felker, sfelker@hudsonalpha.org
PI: Dr. Greg Cooper, gcooper@hudsonalpha.org
Code Maintainer: James Lawlor, jlawlor@hudsonalpha.org
2022-11-11 - initial public release of repository
2023-01-13 - bioRxiv preprint, tagged as biorxiv_20230113
2023-02-21 - Update repository with bioRxiv preprint information. Add HGVS notation to Supplementary Table 1 (see data/Felker2023SuppelementaryTable1_hg38_PE_cassettes_and_elements_annotated.tsv). Change 2022 to 2023 in files and README. Tagged as biorxiv_20230113.2